From the article: "Telecommunications companies are required to give police access to calls under federal law, but many apps that rely solely on internet infrastructure are exempt. Facebook contended Messenger was covered by that exemption."
I think it's good that law enforcement can tap calls if necessary, and I see no convincing reason why the existing law and precedent should not extend to apps like messenger which are used just as traditional phones are by many people. Therefore I'm comfortable extending the law to internet based communications.
The powers granted to government should not be absolute, but there must be powers that are granted, so we debate about what powers to grant. The debate cannot be resolved on an a priori basis using abstract principles, it can only be resolved on a case by case basis. If we only rely on abstract principles we will inevitably be pulled toward absolute power or absolute impotency.